plot_compare_profiles {MutationalPatterns} | R Documentation

## Compare two 96 mutation profiles

### Description

Plots two 96 mutation profiles and their difference, reports the residual sum of squares (RSS).

### Usage

    plot_compare_profiles(profile1, profile2, profile_names = c("profile 1",
      "profile 2"), profile_ymax = 0.2, diff_ylim = c(-0.02, 0.02), colors,
      condensed = FALSE)

### Arguments

`profile1` | First 96 mutation profile
`profile2` | Second 96 mutation profile
`profile_names` | Character vector with names of the mutations profiles used for plotting, default = c("profile 1", "profile 2")
`profile_ymax` | Maximum value of y-axis (relative contribution) for profile plotting, default = 0.2
`diff_ylim` | Y-axis limits for profile difference plot, default = c(-0.02, 0.02)
`colors` | 6 value color vector
`condensed` | More condensed plotting format. Default = F.

### Value

96 spectrum plot of profile 1, profile 2 and their difference

### See Also

`mut_matrix`, `extract_signatures`

### Examples

    ## See the 'mut_matrix()' example for how we obtained the following
    ## mutation matrix.
    mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
                                    package="MutationalPatterns"))

    ## Extracting signatures can be computationally intensive, so
    ## we use pre-computed data generated with the following command:
    # nmf_res <- extract_signatures(mut_mat, rank = 2)

    nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
                        package="MutationalPatterns"))

    ## Compare the reconstructed 96-profile of sample 1 with orignal profile
    plot_compare_profiles(mut_mat[,1],
                            nmf_res$reconstructed[,1],
                            profile_names = c("Original", "Reconstructed"))

[Package MutationalPatterns version 1.6.1 Index]